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    STAG1 STAG1 cohesin complex component [ Homo sapiens (human) ]

    Gene ID: 10274, updated on 27-Nov-2024

    Summary

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    Official Symbol
    STAG1provided by HGNC
    Official Full Name
    STAG1 cohesin complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:11354
    See related
    Ensembl:ENSG00000118007 MIM:604358; AllianceGenome:HGNC:11354
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SA1; MRD47; SCC3A
    Summary
    This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 10.7), endometrium (RPKM 9.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STAG1 in Genome Data Viewer
    Location:
    3q22.3
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (136336236..136752378, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (139076901..139493092, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (136055078..136471220, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135942902-135943448 Neighboring gene ribosomal protein L31 pseudogene 23 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:135968821-135969687 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:136015730-136016305 Neighboring gene propionyl-CoA carboxylase subunit beta Neighboring gene RNA, U6 small nuclear 1284, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:136344516-136345016 Neighboring gene RNY4 pseudogene 4 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 10 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:136442929-136443555 Neighboring gene RNA, U6 small nuclear 789, pseudogene Neighboring gene hESC enhancers GRCh37_chr3:136470665-136471596 and GRCh37_chr3:136471597-136472528 Neighboring gene DNAJC8 pseudogene 2 Neighboring gene STAG1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20588 Neighboring gene sulfotransferase family 1D member 1 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Single Nucleotide Polymorphism Facilitated Down-Regulation of the Cohesin Stromal Antigen-1: Implications for Colorectal Cancer Racial Disparities. Datta S, et al. Neoplasia, 2018 Mar. PMID 29471289, Free PMC Article
    2. STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability. Lehalle D, et al. J Med Genet, 2017 Jul. PMID 28119487
    3. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies. Saitta C, et al. Blood Cancer J, 2022 Jun 2. PMID 35654786, Free PMC Article
    4. Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications. Sakthivel KM, et al. J Environ Pathol Toxicol Oncol, 2021. PMID 33639073
    5. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Richart L, et al. Nucleic Acids Res, 2021 Nov 8. PMID 34648034, Free PMC Article

    See all (93) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
      Title: Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
    2. Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
      Title: Different NIPBL requirements of cohesin-STAG1 and cohesin-STAG2.
    3. Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies.
      Title: Potential role of STAG1 mutations in genetic predisposition to childhood hematological malignancies.
    4. PD-L1 regulates genomic stability via interaction with cohesin-SA1 in the nucleus.
      Title: PD-L1 regulates genomic stability via interaction with cohesin-SA1 in the nucleus.
    5. STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.
      Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells.
    6. STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
      Title: STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers.
    7. Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture.
      Title: Specialized functions of cohesins STAG1 and STAG2 in 3D genome architecture.
    8. Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications.
      Title: Whole Exome Sequencing Identifies Cohesin Component STAG1 Mutation in de novo Acute Myeloid Leukemia (FAB M2): A Pilot Study with Cytogenetics, Clinical and Prognostic Implications.
    9. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
      Title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
    10. Study provides a comprehensive review of the function of STAG1/2 in human physiology and disease and an integrative analysis of available omics data on STAG alterations in a wide array of cancers, comprising 53 691 patients and 1067 cell lines.
      Title: STAG Mutations in Cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual disability, autosomal dominant 47
    MedGen: C4539951 OMIM: 617635 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp781D1416

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of mitotic sister chromatid cohesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in mitotic spindle assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sister chromatid cohesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome TAS
    Traceable Author Statement
    more info
    		  
    located_in chromosome, centromeric region TAS
    Traceable Author Statement
    more info
    		  
    part_of cohesin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of cohesin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of mitotic cohesin complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitotic spindle pole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cohesin subunit SA-1
    Names
    SCC3 homolog 1
    nuclear protein stromal antigen 1
    sister chromatid cohesion 3 homolog A
    stromal antigen 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_005862.3 → NP_005853.2  cohesin subunit SA-1

      See identical proteins and their annotated locations for NP_005853.2

      Status: REVIEWED

      Source sequence(s)
      AC069524, BC017735, BC064699
      Consensus CDS
      CCDS3090.1
      UniProtKB/Swiss-Prot
      O00539, Q6P275, Q8WVM7
      UniProtKB/TrEMBL
      Q4LE48
      Related
      ENSP00000372689.2, ENST00000383202.7
      Conserved Domains (2) summary
      pfam08514
      Location:160 → 268
      STAG; STAG domain
      pfam14621
      Location:3 → 83
      RFX5_DNA_bdg; RFX5 DNA-binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      136336236..136752378 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447229.1 → XP_047303185.1  cohesin subunit SA-1 isoform X1

      Related
      ENSP00000404396.2, ENST00000434713.6

    2. XM_047447228.1 → XP_047303184.1  cohesin subunit SA-1 isoform X1

    3. XM_047447231.1 → XP_047303187.1  cohesin subunit SA-1 isoform X2

    4. XM_047447230.1 → XP_047303186.1  cohesin subunit SA-1 isoform X2

    5. XM_047447235.1 → XP_047303191.1  cohesin subunit SA-1 isoform X3

    6. XM_017005525.2 → XP_016861014.1  cohesin subunit SA-1 isoform X4

      UniProtKB/TrEMBL
      B4E2Q7

    RNA

    1. XR_001739978.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      139076901..139493092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344912.1 → XP_054200887.1  cohesin subunit SA-1 isoform X1

    2. XM_054344911.1 → XP_054200886.1  cohesin subunit SA-1 isoform X1

    3. XM_054344914.1 → XP_054200889.1  cohesin subunit SA-1 isoform X2

    4. XM_054344913.1 → XP_054200888.1  cohesin subunit SA-1 isoform X2

    5. XM_054344915.1 → XP_054200890.1  cohesin subunit SA-1 isoform X3

    6. XM_054344916.1 → XP_054200891.1  cohesin subunit SA-1 isoform X4

    RNA

    1. XR_008486626.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVM7.3 GenPept UniProtKB/Swiss-Prot:Q8WVM7

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